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CHAPTER 3

The Molecules of Life

Today

• General features of organic molecules

• Small biological molecules: Lipids, small sugars, amino acids, nucleotides

Next lecture

• Biological macromolecules: DNA/RNA, proteins, polysaccharides

Last time:

• Refresher of basic chemistry

• Radioactive isotopes in biology and medicine

• The role of water in biology

About formulas

• You don’t have to memorize chemical formulas

• But you need to learn

• names and defining features of main chemical classes,

• the main functional groups,

• the principles of key reactions.

General features of organic molecules

• Are based on carbon skeletons

• Structural versatility: forming a huge number of shapes

• Chemical versatility

• Specific binding

• Carbon

– 4 electrons in the outer shell that holds 8.

– can form up to 4 covalent bonds.

• Carbon can make bonds with

– other carbons forms an endless diversity of carbon skeletons.

– H, O, and N

• Organic chemistry is the study of carbon compounds.

– The rest of the cell consists mostly of carbon-based molecules.

– Carbon is unparalleled in its ability to form the large, complex, diverse molecules that are necessary for life function

Organic molecules = compounds of carbon

Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings

• Hydrocarbons (탄화수소) are the simplest organic compounds. – Contain only carbon and hydrogen atoms. – The simplest hydrocarbon is methane (a greenhouse gas)


• Carbon can form four bonds, enabling chain formation and branching

• Hydrocarbons are the main molecules in gasoline.

• Hydrocarbons in fat provide energy for our bodies.

Structural versatility

• This ability results from the abilities to – form unique three-dimensional shapes. – Functional groups strengthen shape-based intermolecular interactions

"There is only one word that matters in biology, and that is specificity. “ Pioneering molecular biologist Aaron Klug

Specific binding

http://www.molsoft.com/screenshots.html

human β2 adrenergic receptor


Specific binding between biomolecules is the basis of specific functioning

Receptor molecule

Transmitting cell

Receiving cell

Signal molecule

• One nerve cell in brain “talks” to another by releasing signal molecules with a shape that fits receptor molecules located on the surface of the receiving cell


• The properties of organic compounds also depend on the atoms attached to the carbon skeleton. – These atoms create functional groups.

Chemical versatility

Sulfhydryl group (thio group) -SH Found in amino acids

Small bio-molecules: • Lipids • Small sugars • Amino acids • Nucleotides (Bio-molecule = molecule produced by organism)

A tour of the classes of small biomolecules

Lipids

• Lipids are hydrophobic. – They do not mix with water. – Main classes of lipids:

• Fats • Steroids • Membrane lipids (will be introduced in the lecture on membranes)

Lipids


Fats

• Dietary fat consists largely of the molecule triglyceride. – Triglyceride is a combination of glycerol and three fatty acids.

• Functions of fats in the body: – Energy storage – Cushioning – Insulation – Biological signals

Energy storage function of fat

• Many cell types contain fats, but most fat is stored in specialized cells (adipocytes) • Fatty acids are similar to the hydrocarbons of gasoline • Fats have a much higher energy density than sugars

─ store more than twice as much energy per weight ─ do not bind water ─ Total energy density of storage fats is ~6 times higher than that of sugars!

• Without fat stores

─ we would weigh several times more ─ We would have to eat all the time or be not mobile! ─ Fat made us free to focus our life on things other than eating

•Extreme animals illustrate the importance of fat fuels

•Musk shrews have almost no body fat must feed constantly

•Fat fuels allow humming birds to cross the Gulf of Mexico

•Fat fuels allow grizzly bears to hibernate for several months without feeding

Musk shrew Ruby-throated hummingbird Grizzly bear

Fuel Normal weight (70 kg man)

Obese (140 kg man)

Fats (mainly adipose tissue) 141 752

Proteins (mainly muscle) 24 32

Sugars (mainly muscle, liver) 0.90 0.92

Circulating fuels 0.10 0.11

Total 166 785

Survival without food in months 3 14

Energy reserves of humans (in thousands of kcal)

• Obesity facilitates the development of many diseases (Diabetes, Cardiovascular disease, Cancer)

Fats and health

In the USA:


• Saturated fatty acids (especially in animals lard) – Straight chains of hydrocarbons – Saturated fats don’t suppress hunger make you eat more

• Unsaturated fatty acids (especially in plants and fish) – Contain double bonds kinks more liquid

Fat molecule Kink

Unsaturated fatty acid

Saturated fatty acid

• Food manufacturers turn vegetable oil into solid (Margarine and peanut butter)

• This is achieved by adding hydrogen to double bonds (“hydrogenation”)

• But incomplete hydrogenation also creates trans fat

Trans fats are artificial food components

Oleic acid

Elaidic acid

Stearic acid

Intended product in hydrogenation

Product of incomplete hydrogenation

Cis bond

Trans bond

Trans fats are unhealthy • A 2% increase in trans fat consumed, or a

~15% increase in saturated fat consumed doubled risk in coronary heart disease

• Some governments have started to forbid trans fats

Steroids • Steroids are different from fats in structure and function.

– Are classified as lipids because they are hydrophobic

• Functions – Structural: Cholesterol – regulates fluidity of biological membranes – Signaling molecules: cholesterol is precursor of steroid hormones - Regulate

development, growth, metabolism, sexual identity, fertility.

Female sex hormone Male sex hormone

The key culprit in atherosclerosis

The position of this hydrogen atom decided whether you became boy or girl


• Excessive cholesterol leads to atherosclerosis cardiac infarction, stroke

Human coronary artery

Lipid-containing deposits called plaques build up within the walls of blood vessels, reducing blood flow and increasing risk of heart attacks (심장마비) and strokes (뇌졸중)

• Synthetic steroids can build up muscles.

– These steroids are synthetic variants of testosterone

– These substances pose serious health risks.

• Anabolic steroids often reduce the normal output of sex hormones violent mood swings, deep depression, liver damage, high cholesterol, shrunken testicles, reduced sex drive, infertility

Carbohydrates

• Carbohydrates include:

– Small sugar molecules in soft drinks

– Long starch molecules in pasta and potatoes

• Major source of dietary energy

• Building material to form much of the plant body

Carbohydrates


Simple sugars (monosaccharides, disaccharides)

• Monosaccharides (단당류) are simple sugars (mono = single; sacchar = sugar) – Glucose (포도당) is found in sports drinks. – Fructose (과당) is found in fruit.

• Honey contains both glucose and fructose.

Glucose → cellular work → H2O + CO2 • Monosaccharides are an important fuel.

• Glucose and fructose are isomers. – Same formula (C6H12O6), but

atoms are arranged differently. – fructose is sweeter than glucose


• In aqueous solutions, monosaccharides form rings.

Glucose Fructose


Disaccharides

• Are constructed from two monosaccharides.

• Are joined through a dehydration reaction.

• Main disaccharides

– Maltose (glucose + glucose) - abundant in beer

– Lactose (galactose + glucose) – abundant in milk

– Sucrose (glucose + fructose) – abundant in soft drinks, cakes, …

• Lactose (“milk sugar) - Most adult mammals cannot digest milk sugar ( “Lactose intolerance”) - ~7,000 years ago, in a European population with a pastoral

lifestyle a mutation led to the ability to digest lactose at adult age.

Now ~35% of adult humans can drink milk

http://www.nature.com/news/archaeology-the-milk-revolution-1.13471

- Similar mutations occurred in some other parts of the world

• Sucrose (“table sugar”) – Consists of a glucose linked to a fructose. – Is extracted from sugar cane and the roots of sugar beets. – In the gut, sucrose is rapidly digested into fructose and glucose.

Sweet sugars are unhealthy • Eating too much fructose is seen as a major

reason for chronic metabolic disease (obesity, diabetes, heart disease…) – Fructose is very abundant in corn syrup. – Fructose is also produced from the digestion

of table sugar (sucrose). – Especially abundant in soft drinks – avoid!

http://canadianwayfarer.wordpress.com/2013/07/14/a-blight-on-the-developing-world/

http://epianalysis.wordpress.com/2013/03/29/globalsoda/

Sugar consumption 2007 Occurrence of obesity 2008

http://epianalysis.wordpress.com/2013/03/29/globalsoda/

Soft drink consumption

Occ

urre

nce

of o

verw

eigh

t

Data points = countries

Amino acids

• Amino acids are small organic molecules with two functional groups: -NH2 and -COOH

• They are the building blocks of proteins

Amino acids


The Monomers: Amino Acids • There are 20 common amino acids and a few very rare ones.

• They are abbreviated with a three-letter or one-letter code

• Each amino acid contains two functional groups (amino and carboxyl), a central carbon atom, and a variable side group.

• The side groups defines the identity and specific properties of an amino acid

Acidic

Neutral-non-polar

Basic

Neutral-polar

20 amino acids: classified by polarity of the side groups

Amino acids and human nutrition

• Of the 20 common amino acids, 8 amino acids cannot be synthesized by adult humans (“essential amino acids”) need to be provided with the food

• Unlike fats or sugars, the human body does not store amino acids for reserve

• Therefore the amount of muscle protein you can build is limited by the amount essential amino acids you eat

Body builders need essential amino acids as nutritional supplements

Water level = muscle mass

Amount of least abundant essential amino acid

• Even if only one essential amino acid is missing in the food, the body will lose muscle mass

Nucleotides

• Are small organic molecules consisting of three parts: a sugar, a phosphate, a “base”

• Are the building blocks of nucleic acids

Nucleotides


• This sugar is made of 5 C atoms (“pentose”)

• This sugar comes in two important versions: Either -H or -OH in this position

• The bases come in four major versions

• Each DNA nucleotide has one of the following bases

Summary – “Small” biomolecules

•Biomolecules are organic molecules that are typically synthesized by organisms •Organic molecules are carbon-based. Carbon can form chains and branches and functional groups (hydroxyl, carbonyl, amino, carboxyl, sulfhydryl). The simplest organic molecules are hydrocarbons (C and H only), which are energy-rich. •Chain formation allows formation of complex shapes; functional groups provide chemical versatility and polarity. •Shape and polarity allow specific binding, a most fundamental property of biomolecules.

•Lipids are defined by their hydrophobicity and comprise “fats” and steroids: •“Fats” (triglycerides) are formed from 1 glycerol and 3 fatty acids and store the bulk of energy in animals. But due to their poor solubility this energy is more difficult to access than from sugars. • Benefit for health: Non-saturated (cis) fatty acids > saturated fatty acids > trans-fatty acids. •The simplest steroid is cholesterol, which is important for the cell surface, but too much facilitates atherosclerosis. Steroid hormones, which are derived from cholesterol, are key regulators of development, metabolism, sex; synthetic steroids can boost muscle growth but have bad side effects.

•Small carbohydrates (sugars) include monosaccharides and disaccharides •Mono: Glucose, fructose, and others. Di: Lactose, sucrose, and others. •Sugars are well water soluble and a preferred energy source, but not stored in large amounts (animals). •Overeating of fructose (in corn syrup, table sugar, soft drinks) has become a major health problem.

•Amino acids contain 1 amino group (-NH2), 1 carboxyl group (-COOH), and 1 side group •Total of 20 side groups, making the amino acid neutral-nonpolar, neutral-polar, acidic, or basic. •Amino acids are not stored for reserve, and humans can synthesize many but not all of them.

•Nucleotides contain 1 N-rich “base”, 1 pentose (sugar with 5 C atoms), and a phosphate group •The pentose comes in 2 main versions: with or without an oxygen at carbon atom number 2. •The base comes in 4 main versions, and the resulting nucleotides are called A, T (U), G, or C.

• 생분자는 일반적으로 유기체들에 의해 합성되는 유기분자이다.

• 유기분자는 탄소를 기반에 두고 있다. 탄소는 사슬기와 가지기, 그리고 기능기 (히드록실기, 카르보닐기, 아미노기, 카르복실기, 설프히드릴기)를 가지고 있다. 가장 단순한 유기분자는 에너지가 풍부한, 탄화수소 (C와 H로만 구성)이다. • 사슬형성은 복잡한 형태의 형성을 이끈다; 기능기는 화학적 다양성과 극성을 제공한다. • 모양과 극성으로 인하여 생분자의 가장 기본적인 특성인 특이적 결합이 가능하다.

• 지질류는 소수성에 의해 정의되며, “지방” 과 스테로이드로 구성된다.

• “지방” (트리글리세라이드) 은 1 분자의 글리세롤과 3 분자의 지방산으로 구성되며, 에너지원으로서 동물의 몸에 저장된다. 그러나 낮은 용해성 때문에 이 에너지는 당보다 더 이용하기 어렵다. • 건강에 대한 이익: 불포화 (시스형) 지방산 > 포화 지방산 > 트랜스 지방산 • 가장 단순한 스테로이드는 콜레스테롤이며, 세포 표면에 중요한 역할을 하나, 과하면 동맥경화를 유발할 수 있다. 콜레스테롤로부터 유래된 스테로이드 호르몬들은 발달과 신진대사, 성에서 중요한 조절역할을 한다; 합성 스테로이드는 근육 성장을 촉진할 수 있으나, 많은 부작용들을 가지고 있다.

• 작은 탄수화물 (당류)은 단당류와 이당류로 구성된다.

• 단당류: 포도당, 과당 등. 이당류: 젖당, 자당(설탕) 등. • 당류는 물에 잘 녹으며, 에너지원으로 선호되나, 동물의 경우 많은 양으로 저장되지 않는다. • 과당 (옥수수 시럽, 설탕, 청량음료 등)의 과섭취는 건강에 큰 문제를 일으킬 수 있다.

• 아미노산은 1개의 아미노 그룹 (-NH2)과, 1개의 카르복실 그룹 (-COOH), 1개의 곁사슬(side chain)이 있다.

• 총 20가지의 곁사슬은 아미노산을 중성·비극성, 중성·극성, 산성, 또는 염기성으로 만든다. • 아미노산은 예비로 저장되지 않으며, 인간은 많은 종류를 스스로 생산할 수 있으나, 모두 합성하지는 못한다.

• 핵산은 1 개의 N이 많은 “염기”와, 1개의 펜토오스 (5탄당), 그리고 1개의 인산기를 가지고 있다.

• 펜토오스는 2 종류가 있다: 2번 탄소 원자에 산소의 유무에 따라 달라진다. • 염기는 4 종류가 있으며, 이들을 A, T (U), G 또는 C 라고 부른다.

요약- “작은”생분자

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